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Segmentation violation error with hmmsearch (died with <Signals.SIGSEGV: 11>) #60

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francis29029 opened this issue Jan 29, 2021 · 3 comments
Closed

Segmentation violation error with hmmsearch (died with <Signals.SIGSEGV: 11>) #60

francis29029 opened this issue Jan 29, 2021 · 3 comments

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@francis29029
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hello,

While annotating some mags I encounter this error with the hmmsearch. Does any of you already encounter this error using DRAM and could possibly help ?

ps: my dram setup work and I already annotated dataset of 350 MAGs. But sometimes, rarely, for some MAGs, I encounter this error.

According google it's a "segmentation violation" and it's link with some memory issues....

subprocess.CalledProcessError: Command '['hmmsearch', '--domtblout', 'genomes/annotations/dram/intermediate_files/MAG130/working_dir/MAG130/tmp/kofam_profile.b6', '--cpu', '8', '/Software/python/Anaconda3-2020.11-DRAM/DRAM_data_1/kofam_profiles.hmm', 'genomes/annotations/dram/intermediate_files/MAG130/working_dir/MAG130/tmp/genes.faa']' died with <Signals.SIGSEGV: 11>.

Thanks a lot

Francis
@javadgh6
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I had the same problem. change hmmer from 3.3.1 version to 3.1b2 will solve the problem.

@francis29029
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Hello, thanks for your reply ! hum the 3.1b2 is very old version (2015) no ?

Then by searching "hmmer and segmentation fault", I was able to find out other similar issues ? (which I did not find the first time):
#34
#39

and now I do not know if there is really a solution to this segmentation fault (seems it depends of the system). We are using the hmmer 3.3.1 version. Does upating to 3.3.2 (last release might solved the issue ?)

here is the output of conda list

packages in environment at /nihs/Software/python/Anaconda3-2020.11-DRAM/envs/DRAM:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
altair 4.1.0 py_1 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
barrnap 0.9 3 bioconda
bedtools 2.29.2 hc088bd4_0 bioconda
brotlipy 0.7.0 py39h38d8fee_1001 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h36c2ea0_0 conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
cachecontrol 0.12.6 py_0 conda-forge
certifi 2020.12.5 py39hf3d152e_0 conda-forge
cffi 1.14.4 py39he32792d_1 conda-forge
chardet 3.0.4 py39h079e4ff_1008 conda-forge
cryptography 3.2.1 py39h01d1d65_0 conda-forge
curl 7.71.1 he644dc0_8 conda-forge
cycler 0.10.0 py_2 conda-forge
cython 0.29.21 py39hfbd4741_1 conda-forge
decorator 4.4.2 py_0 conda-forge
dram-bio 1.1.1 dev_0
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
et_xmlfile 1.0.1 py_1001 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
freetype 2.10.4 h7ca028e_0 conda-forge
gawk 5.1.0 h516909a_0 conda-forge
gdbm 1.18 h0a1914f_2 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
git 2.29.2 pl5320h78be0e9_1 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
hdmedians 0.14.1 py39h1dff97c_1 conda-forge
hmmer 3.3.1 he1b5a44_0 bioconda
idna 2.10 pyh9f0ad1d_0 conda-forge
importlib-metadata 3.1.1 pyhd8ed1ab_0 conda-forge
importlib_metadata 3.1.1 hd8ed1ab_0 conda-forge
infernal 1.1.3 h516909a_0 bioconda
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipython 7.19.0 py39hef51801_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jdcal 1.4.1 py_0 conda-forge
jedi 0.17.2 py39hf3d152e_1 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
joblib 0.17.0 py_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
jsonschema 3.2.0 py_2 conda-forge
kiwisolver 1.3.1 py39h081fc7a_0 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.11 hcbb858e_1 conda-forge
ld_impl_linux-64 2.35.1 hed1e6ac_0 conda-forge
libblas 3.9.0 3_openblas conda-forge
libcblas 3.9.0 3_openblas conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
libgfortran-ng 9.3.0 he4bcb1c_17 conda-forge
libgfortran5 9.3.0 he4bcb1c_17 conda-forge
libgomp 9.3.0 h5dbcf3e_17 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn2 2.3.0 h516909a_0 conda-forge
liblapack 3.9.0 3_openblas conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
libtiff 4.1.0 h4f3a223_6 conda-forge
libunistring 0.9.10 h14c3975_0 conda-forge
libwebp-base 1.1.0 h36c2ea0_3 conda-forge
lockfile 0.12.2 py_1 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
markupsafe 1.1.1 py39h38d8fee_2 conda-forge
matplotlib-base 3.3.3 py39h98787fa_0 conda-forge
mmseqs2 12.113e3 h2d02072_2 bioconda
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.0 py39h081fc7a_2 conda-forge
natsort 7.1.0 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
networkx 2.5 py_0 conda-forge
numpy 1.19.4 py39h57d35e7_1 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openpyxl 3.0.5 py_0 conda-forge
openssl 1.1.1h h516909a_0 conda-forge
packaging 20.7 pyhd3deb0d_0 conda-forge
pandas 1.1.5 py39hde0f152_0 conda-forge
parallel 20201122 ha770c72_0 conda-forge
parso 0.7.1 pyh9f0ad1d_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 8.0.1 py39h397ff4d_0 conda-forge
pip 20.3.1 pyhd8ed1ab_0 conda-forge
pluggy 0.13.1 py39h079e4ff_3 conda-forge
prodigal 2.6.3 h516909a_2 bioconda
prompt-toolkit 3.0.8 pyha770c72_0 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.9.0 pyh9f0ad1d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.7.3 pyhd8ed1ab_0 conda-forge
pyopenssl 20.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrsistent 0.17.3 py39hbd71b63_1 conda-forge
pysocks 1.7.1 py39h079e4ff_2 conda-forge
pytest 6.1.2 py39hf3d152e_0 conda-forge
python 3.9.1 hffdb5ce_1_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.9 1_cp39 conda-forge
pytz 2020.4 pyhd8ed1ab_0 conda-forge
readline 8.0 he28a2e2_2 conda-forge
requests 2.25.0 pyhd3deb0d_0 conda-forge
ruby 2.7.2 he592edb_3 conda-forge
scikit-bio 0.5.6 py39h16ac069_4 conda-forge
scikit-learn 0.23.2 py39hf3c863f_3 conda-forge
scipy 1.5.3 py39hee8e79c_0 conda-forge
setuptools 49.6.0 py39h079e4ff_2 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlalchemy 1.3.20 py39h07f9747_0 conda-forge
sqlite 3.34.0 h74cdb3f_0 conda-forge
threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
toolz 0.11.1 py_0 conda-forge
tornado 6.1 py39hbd71b63_0 conda-forge
traitlets 5.0.5 py_0 conda-forge
trnascan-se 2.0.7 pl526h516909a_0 bioconda
tzdata 2020d h516909a_0 conda-forge
urllib3 1.25.11 py_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wget 1.20.1 h22169c7_0 conda-forge
wheel 0.36.1 pyhd3deb0d_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
zipp 3.4.0 py_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.4.5 h6597ccf_2 conda-forge

SilasK added a commit to bioconda/bioconda-recipes that referenced this issue Feb 1, 2021
@SilasK
fix WrightonLabCSU/DRAM#60
6446334
@SilasK SilasK mentioned this issue Feb 1, 2021
Merged
BiocondaBot pushed a commit to bioconda/bioconda-recipes that referenced this issue Feb 3, 2021
@SilasK
[ci skip] Merge PR 26513
90b3c80 
Merge PR #26513, commits were: 
 * increase build number
 * create hmmer 3.3.2
 * fix WrightonLabCSU/DRAM#60
@shafferm
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Looks like this has been fixed. Sorry for missing your issue earlier but glad it got figured out!

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@shafferm @francis29029 @javadgh6